From WikiPathways

Revision as of 19:32, 15 April 2014

This guide describes the most common uses of various elements of the WikiPathways editor palette. Examples are taken directly from the WikiPathways archives. If you have questions about specific cases, contact the discussion mailing list.

Interactions

Line / Arrow

The solid line and arrow are used to denote a variety of processes, including conversion, translocation, activation, binding and modification.

Enzymatic conversion	Receptor binding	Translocation between compartments	Activation by cAMP

Dashed line / dashed arrow

The dashed line and arrow are used to denote an uncertain process or a process that involves additional steps not outlined in the current diagram.

Multi-step process without details

T-bar

The T-bar is used to denote inhibition.

Line types

Any interaction can have a line style of either straight, curved, elbow or segmented. The default style is straight, and is shown in the examples above. The other three line styles are used primarily to increase readability of complex pathways.

Curved	Elbow	Segmented

Interactions - Molecular Interaction Maps (MIM)

The WikiPathways editor includes a set of MIM interaction types, based on the Molecular Interaction Maps notation.

Necessary stimulation

Binding

Conversion

Stimulation

Catalysis

Transcription-Translation

Data nodes

The below image shows the preferred usage for the most common data node types:

• GeneProduct: Default data node and should be used for any gene product.
• Metabolite: Should be used for any metabolite, drug or small molecule.
• Pathway: Should be used instead of a label to denote a connection to another pathway.

Graphical elements

Label

Line

Arc

Rectangle

Cellular compartments

Cell

Nucleus

Vesicle